Issue running Markov jumps with BEAST file generated in Beauti 1.8.1

[Jane Hawkey]

I'm attempting to run a Markov Jumps beast run on two different traits (pos1 and pos2) in BEAST v1.7.5 using an xml file generated by Beauti 1.8.1

This is the error it's giving me:

Parsing error - poorly formed BEAST file, test_IStraits_220914_181.xml:

Error parsing '<logTree>' element with id, 'treeFileLog':

Trait named, pos1.count, not found for MarkovJumpsBeagleTreeLikelihood(treeLikelihood[pos1.treeLikelihood])

I attempted to add the following code to the xml file but that didn't seem to help:

<log id="cjh" logEvery="1000" fileName="test_ISTraits_take2.cjh.txt">

      <completeHistoryLogger>

        <MarkovJumpsBeagleTreeLikelihood idref="pos1.treeLikelihood"/>

      </completeHistoryLogger>

            <completeHistoryLogger>

        <MarkovJumpsBeagleTreeLikelihood idref="pos2.treeLikelihood"/>

      </completeHistoryLogger>

</log>

[Andrew Rambaut]

Generally it isn’t always possible to run XML generated in one version of BEAUti in an older version of BEAST. Some models were not implemented

in older versions or the format has changed. Bugs are also fixed. Use BEAST v1.8.1 for this.

Andrew

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Andrew Rambaut 

Institute for Evolutionary Biology | Centre for Infection, Immunity & Evolution 

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH3 9JT, UK

contact – a.ra...@ed.ac.uk | http://tree.bio.ed.ac.uk | tel +44 131 6508624

[Jane Hawkey]

I've attempted to use BEAST v1.8.1 but am still running into parsing errors. The xml file was generated with Beauti v1.8.1 also.

This is the latest:

dr.xml.XMLParseException: Object with Id=count already exists

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.parse(Unknown Source)

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)

Sep 23, 2014 10:02:04 AM dr.app.beast.BeastMain <init>

SEVERE: Parsing error - poorly formed BEAST file, test_IStraits_230914_181.xml:

Object with Id=count already exists

java.lang.RuntimeException: Terminate

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)

I have removed the sections of the xml file that relate to creating a tree and replaced it with an empirical tree model, as I have a .trees that I want to use rather than generating the tree with the traits. Not sure if that is causing issues with the count variable.

[Jane Hawkey]

Never mind, I fixed my problem.

There were extra <parameter> tags for the state changes for the different positions, and this is what was causing that error.

[Pauline Faure]

Hello,

I have the same problem and can't manage to fix it.
My file is generated with Beauti 1.8.1 and ran with Beast 1.8.1. This is what I get...

BEAST has terminated with an error.

dr.xml.XMLParseException: Error parsing '<logTree>' element with id, 'treeFileLog':
Trait named, location.count, not found for MarkovJumpsBeagleTreeLikelihood(treeLikelihood[location.treeLikelihood])

    at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)

    at dr.xml.XMLParser.convert(Unknown Source)
    at dr.xml.XMLParser.convert(Unknown Source)
    at dr.xml.XMLParser.convert(Unknown Source)
    at dr.xml.XMLParser.parse(Unknown Source)
    at dr.app.beast.BeastMain.<init>(Unknown Source)
    at dr.app.beast.BeastMain.main(Unknown Source)

Apr 15, 2015 6:19:40 PM dr.app.beast.BeastMain <init>

SEVERE: Parsing error - poorly formed BEAST file, location_markov_nigeria_59seq_120M.xml:

Error parsing '<logTree>' element with id, 'treeFileLog':

Trait named, location.count, not found for MarkovJumpsBeagleTreeLikelihood(treeLikelihood[location.treeLikelihood])

java.lang.RuntimeException: Terminate

    at dr.app.beast.BeastMain.<init>(Unknown Source)
    at dr.app.beast.BeastMain.main(Unknown Source)

Thank you for your help!

Pauline